PDB-7c9m: The structure of product-bound CntL, an aminobutyrate transferase...

ID or keywords:

Entry

Database: PDB / ID: 7c9m

Title

The structure of product-bound CntL, an aminobutyrate transferase in staphylopine biosynthesis

Components

D-histidine 2-aminobutanoyltransferase

Keywords

TRANSFERASE / Metallophore / Biosynthesis / product / Aminobutyrate

Function / homology

D-histidine 2-aminobutanoyltransferase / nicotianamine synthase activity / nicotianamine biosynthetic process / Nicotianamine synthase / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Chem-FN6 / 5'-DEOXY-5'-METHYLTHIOADENOSINE / D-histidine 2-aminobutanoyltransferase

Function and homology information

Biological species

Staphylococcus aureus subsp. aureus Mu50 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Luo, Z. / Zhou, H.

Funding support

China, 1items

Citation

Journal: Faseb J. / Year: 2021
Title: Structural insights into the ligand recognition and catalysis of the key aminobutanoyltransferase CntL in staphylopine biosynthesis.
Authors: Luo, Z. / Luo, S. / Ju, Y. / Ding, P. / Xu, J. / Gu, Q. / Zhou, H.

History

Deposition	Jun 6, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 28, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7c9m.cif.gz	412.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7c9m.ent.gz	342 KB	Display	PDB format
PDBx/mmJSON format	7c9m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7c9m_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7c9m_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7c9m_validation.xml.gz	37 KB	Display
Data in CIF	7c9m_validation.cif.gz	48.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c9/7c9m ftp://data.pdbj.org/pub/pdb/validation_reports/c9/7c9m	HTTPS FTP

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Related structure data

Related structure data	7c7mSC 7c9kC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1u9e-1 3qt0-d 2p40-d 1af2-d 5qio-d 3b89-d 2pxa-2 3et2-2 1ctt-d 6st0-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

7c7mSC

7c9kC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: D-histidine 2-aminobutanoyltransferase

B: D-histidine 2-aminobutanoyltransferase

C: D-histidine 2-aminobutanoyltransferase

D: D-histidine 2-aminobutanoyltransferase

hetero molecules

130 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-histidine 2-aminobutanoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
32.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: D-histidine 2-aminobutanoyltransferase

hetero molecules

defined by author&software
32.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: D-histidine 2-aminobutanoyltransferase

hetero molecules

defined by author&software
32.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: D-histidine 2-aminobutanoyltransferase

hetero molecules

defined by author&software
32.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.519, 96.684, 211.428
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	D-histidine 2-aminobutanoyltransferase / Nicotianamine synthase-like enzyme / NAS Mass: 31858.998 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: Mu50 / Gene: cntL, SAV2469 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H3JXA8, D-histidine 2-aminobutanoyltransferase
#2: Chemical	ChemComp-FN6 / (2S)-2-azanyl-4-[[(2R)-3-(1H-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid Mass: 256.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₁₀H₁₆N₄O₄
#3: Chemical	ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE Mass: 297.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.19 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3 M Magnesium formate dihydrate, 26% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 34032 / % possible obs: 96.8 % / Redundancy: 6.2 % / CC_1/2: 0.998 / R_merge(I) obs: 0.065 / Net I/σ(I): 31.9
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 3435 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7C7M

7c7m

Resolution: 2.7→49.9 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.896 / SU B: 37.081 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R: 7.198 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.285	1680	5 %	RANDOM
R_work	0.24204	-	-	-
obs	0.24423	32206	96.83 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 82.731 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.61 Å²	0 Å²	0 Å²
2-	-	3.46 Å²	-0 Å²
3-	-	-	-2.84 Å²

Refinement step

Cycle: 1 / Resolution: 2.7→49.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7860	0	152	22	8034

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.014	8160
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	7167
X-RAY DIFFRACTION	r_angle_refined_deg	0.771	1.664	11115
X-RAY DIFFRACTION	r_angle_other_deg	0.699	1.661	16632
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.862	5	1025
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.54	24.031	387
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.785	15	1286
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.9	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.031	0.2	1165
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	9325
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1515
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.65	5.235	4112
X-RAY DIFFRACTION	r_mcbond_other	0.651	5.235	4111
X-RAY DIFFRACTION	r_mcangle_it	1.204	7.85	5133
X-RAY DIFFRACTION	r_mcangle_other	1.204	7.85	5134
X-RAY DIFFRACTION	r_scbond_it	0.422	5.283	4048
X-RAY DIFFRACTION	r_scbond_other	0.422	5.284	4049
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	0.774	7.922	5983
X-RAY DIFFRACTION	r_long_range_B_refined	2.69	61.667	8863
X-RAY DIFFRACTION	r_long_range_B_other	2.69	61.668	8864
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	123	-
R_work	0.33	2404	-
obs	-	-	99.41 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.2853	-0.5917	-2.8775	4.9288	0.8781	12.1746	-0.1698	-0.2495	-0.637	0.5453	-0.0442	-0.1179	0.671	0.3039	0.214	0.2313	-0.0347	0.0684	0.088	0.1092	0.321	69.3383	73.4332	147.6845
2	1.5125	0.414	0.0061	8.0123	2.4196	3.6461	-0.2178	-0.0631	-0.0799	0.3775	0.1214	0.3916	0.4249	-0.1656	0.0964	0.1336	-0.0544	0.0997	0.0793	-0.0401	0.1588	64.0083	82.6345	147.5883
3	0.0549	0.016	-0.1415	0.0475	0.0362	0.6312	0.0084	-0.2305	-0.0402	-0.0716	-0.0544	-0.1403	-0.4364	0.717	0.046	0.7263	-0.2657	-0.2226	1.0491	0.2165	0.8284	70.259	96.887	133.7877
4	3.0002	-0.7264	-0.0769	3.1808	0.6836	4.2835	-0.1269	0.5532	0.1972	-0.1676	-0.0614	0.3976	-0.2878	-0.5227	0.1883	0.0456	-0.0184	-0.0023	0.2217	-0.0195	0.2379	58.8785	92.538	134.0786
5	6.5193	-0.2713	1.4657	0.9734	-0.1139	8.8795	0.1271	0.132	0.6503	0.5977	-0.3748	-0.1498	-1.31	0.0736	0.2477	0.7903	-0.0536	-0.0806	0.3215	-0.0277	0.3019	46.697	67.6979	110.0954
6	1.2204	-1.1371	-0.513	8.4283	-0.5099	4.9667	-0.2187	0.3699	-0.3297	0.823	0.0303	-0.3817	-0.2526	0.3581	0.1885	0.2244	-0.0813	-0.0469	0.3321	-0.0159	0.282	50.9698	52.5792	107.6739
7	0.9671	-0.8027	-1.7282	5.4726	0.8834	7.0028	-0.2668	0.0163	-0.1132	0.3212	-0.2901	-0.4363	0.8085	0.6742	0.5569	0.1527	0.1124	0.0185	0.2872	0.189	0.4228	59.8813	43.5028	99.3632
8	3.9124	-1.7056	-2.7957	5.9104	1.4249	7.4692	0.0152	0.3033	0.3128	-0.2602	-0.3159	-0.7237	-0.5017	0.4074	0.3007	0.0589	-0.0279	-0.0024	0.2401	0.1019	0.2887	56.1491	57.1443	89.0729
9	3.5978	0.0336	-1.1938	2.0135	-2.7337	4.1025	-0.3373	-0.6141	-0.0677	0.0539	0.6204	0.2115	0.0311	-0.8044	-0.2832	0.1826	0.0948	0.2395	0.755	0.0703	0.3596	25.414	47.0707	162.9994
10	6.2908	0.5844	2.562	5.1077	-0.3085	5.2629	-0.0486	-0.5189	-0.1427	-0.2718	0.0426	0.1744	-0.051	-0.6509	0.006	0.1259	0.0971	0.1044	0.1836	0.0796	0.1555	33.9174	51.9677	157.4625
11	5.0831	0.4881	-1.1163	2.7344	-1.4384	7.9189	-0.3447	-0.2867	0.4108	0.015	0.0997	-0.059	-0.4258	0.4383	0.245	0.2087	-0.039	-0.0206	0.0613	0.0156	0.2333	48.1196	61.0155	151.1466
12	4.9365	0.3502	-1.2858	2.5715	-1.3742	6.3977	-0.4144	0.6652	0.3646	-0.4618	0.2715	0.4021	-0.2318	-0.7625	0.1429	0.2277	0.0001	-0.056	0.1875	0.1009	0.2292	35.1828	56.4718	140.5353
13	0.6678	-0.152	0.3028	4.0372	-3.3257	2.8308	-0.4459	0.3461	-0.1453	-0.4866	0.4445	0.2128	0.2009	-0.3707	0.0014	0.543	-0.1752	-0.1905	1.329	-0.4097	0.7743	25.2745	38.8507	113.1838
14	7.6721	-0.7839	-4.2182	2.4212	-1.2809	3.5971	-0.5075	1.538	-1.0554	-0.5003	-0.0208	0.1527	0.7396	-1.0246	0.5284	0.4822	-0.2465	0.0759	0.6107	-0.306	0.4982	34.9471	33.1249	113.1425
15	7.2754	-3.2268	6.5523	1.4549	-2.9218	6.0165	-0.6075	0.1003	0.6466	0.3479	-0.0975	-0.3686	-0.4228	0.3147	0.7049	0.7599	-0.0573	-0.015	0.6976	0.0747	0.6283	42.7979	40.6797	127.2447
16	4.3227	-1.5379	-2.0719	2.1472	0.8662	5.3196	-0.7443	-0.0723	-1.2758	0.4261	-0.169	0.2488	1.1569	-0.1264	0.9133	0.5928	-0.1205	0.291	0.1835	0.0906	0.6833	41.3689	28.8082	129.6968

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 62
2	X-RAY DIFFRACTION	2	A	63 - 104
3	X-RAY DIFFRACTION	3	A	105 - 119
4	X-RAY DIFFRACTION	4	A	120 - 264
5	X-RAY DIFFRACTION	5	B	7 - 69
6	X-RAY DIFFRACTION	6	B	70 - 113
7	X-RAY DIFFRACTION	7	B	116 - 182
8	X-RAY DIFFRACTION	8	B	183 - 264
9	X-RAY DIFFRACTION	9	C	7 - 58
10	X-RAY DIFFRACTION	10	C	59 - 115
11	X-RAY DIFFRACTION	11	C	116 - 182
12	X-RAY DIFFRACTION	12	C	183 - 263
13	X-RAY DIFFRACTION	13	D	14 - 57
14	X-RAY DIFFRACTION	14	D	68 - 100
15	X-RAY DIFFRACTION	15	D	101 - 118
16	X-RAY DIFFRACTION	16	D	119 - 264

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